Starting phenix.real_space_refine on Sun Apr 7 19:50:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdw_41175/04_2024/8tdw_41175_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdw_41175/04_2024/8tdw_41175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdw_41175/04_2024/8tdw_41175.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdw_41175/04_2024/8tdw_41175.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdw_41175/04_2024/8tdw_41175_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdw_41175/04_2024/8tdw_41175_neut.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 12 5.49 5 S 29 5.16 5 C 6978 2.51 5 N 2135 2.21 5 O 2203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11359 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3346 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 650 Unresolved non-hydrogen dihedrals: 428 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 15, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 286 Chain: "B" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3371 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 502 Unresolved non-hydrogen angles: 639 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 283 Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 2261 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 407} Link IDs: {'PTRANS': 22, 'TRANS': 435} Chain breaks: 1 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1567 Unresolved non-hydrogen angles: 2002 Unresolved non-hydrogen dihedrals: 1327 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 35, 'TYR:plan': 22, 'ASN:plan1': 19, 'TRP:plan': 5, 'HIS:plan': 16, 'PHE:plan': 20, 'GLU:plan': 32, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 894 Chain: "F" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 2128 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 382} Link IDs: {'PTRANS': 21, 'TRANS': 409} Chain breaks: 2 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1472 Unresolved non-hydrogen angles: 1882 Unresolved non-hydrogen dihedrals: 1248 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'GLN:plan1': 19, 'ASP:plan': 32, 'TYR:plan': 20, 'ASN:plan1': 16, 'TRP:plan': 5, 'HIS:plan': 16, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 835 Chain: "J" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 1} Chain: "K" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 5} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.83, per 1000 atoms: 0.60 Number of scatterers: 11359 At special positions: 0 Unit cell: (109.154, 115.152, 129.546, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 29 16.00 P 12 15.00 O 2203 8.00 N 2135 7.00 C 6978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.58 Conformation dependent library (CDL) restraints added in 2.5 seconds 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3436 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 15 sheets defined 58.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.790A pdb=" N TYR A 154 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 186 removed outlier: 3.820A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.677A pdb=" N LEU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 248 Processing helix chain 'A' and resid 249 through 257 removed outlier: 4.437A pdb=" N VAL A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 removed outlier: 4.733A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 removed outlier: 5.969A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.690A pdb=" N PHE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 373 Processing helix chain 'A' and resid 376 through 393 removed outlier: 3.674A pdb=" N ILE A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.815A pdb=" N ILE A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 424 through 432 removed outlier: 4.053A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 450 removed outlier: 3.548A pdb=" N ILE A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 4.769A pdb=" N GLU A 474 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.675A pdb=" N GLU A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 4.269A pdb=" N ASN A 535 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.754A pdb=" N TYR B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 186 removed outlier: 3.718A pdb=" N HIS B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 206 Processing helix chain 'B' and resid 214 through 220 removed outlier: 4.237A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 232 through 248 Processing helix chain 'B' and resid 249 through 258 removed outlier: 4.352A pdb=" N VAL B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 274 removed outlier: 4.251A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 6.059A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.501A pdb=" N TRP B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 378 through 393 Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 410 through 414 removed outlier: 4.146A pdb=" N ILE B 413 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.988A pdb=" N LYS B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 432 removed outlier: 4.108A pdb=" N LEU B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 450 removed outlier: 3.865A pdb=" N ILE B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 481 removed outlier: 4.348A pdb=" N LYS B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 498 removed outlier: 3.552A pdb=" N PHE B 498 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 576 Processing helix chain 'B' and resid 583 through 588 removed outlier: 3.525A pdb=" N ILE B 587 " --> pdb=" O GLY B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.676A pdb=" N ASN B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 595 through 600' Processing helix chain 'E' and resid 129 through 137 removed outlier: 3.984A pdb=" N ASP E 137 " --> pdb=" O VAL E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.998A pdb=" N ARG E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 154 Processing helix chain 'E' and resid 163 through 186 removed outlier: 3.636A pdb=" N HIS E 167 " --> pdb=" O ASN E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 190 Processing helix chain 'E' and resid 192 through 204 removed outlier: 3.511A pdb=" N VAL E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 220 removed outlier: 3.764A pdb=" N ASP E 218 " --> pdb=" O SER E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 226 removed outlier: 3.896A pdb=" N ARG E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 249 removed outlier: 3.587A pdb=" N GLY E 236 " --> pdb=" O THR E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 257 Processing helix chain 'E' and resid 260 through 274 removed outlier: 4.423A pdb=" N CYS E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 324 Processing helix chain 'E' and resid 330 through 337 Processing helix chain 'E' and resid 355 through 373 Processing helix chain 'E' and resid 377 through 393 Processing helix chain 'E' and resid 394 through 396 No H-bonds generated for 'chain 'E' and resid 394 through 396' Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 411 through 414 removed outlier: 3.897A pdb=" N ASP E 414 " --> pdb=" O THR E 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 411 through 414' Processing helix chain 'E' and resid 415 through 420 Processing helix chain 'E' and resid 424 through 432 Processing helix chain 'E' and resid 438 through 450 removed outlier: 3.675A pdb=" N ILE E 444 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 482 removed outlier: 3.622A pdb=" N TYR E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 474 " --> pdb=" O ARG E 470 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER E 475 " --> pdb=" O GLU E 471 " (cutoff:3.500A) Proline residue: E 477 - end of helix Processing helix chain 'E' and resid 558 through 576 Processing helix chain 'E' and resid 583 through 588 Processing helix chain 'E' and resid 591 through 594 Processing helix chain 'E' and resid 595 through 600 removed outlier: 4.317A pdb=" N ASN E 599 " --> pdb=" O LYS E 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'F' and resid 145 through 147 No H-bonds generated for 'chain 'F' and resid 145 through 147' Processing helix chain 'F' and resid 152 through 157 removed outlier: 3.701A pdb=" N VAL F 156 " --> pdb=" O GLY F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 186 Processing helix chain 'F' and resid 187 through 190 Processing helix chain 'F' and resid 192 through 205 removed outlier: 3.783A pdb=" N VAL F 196 " --> pdb=" O SER F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 214 through 221 removed outlier: 3.704A pdb=" N ASP F 218 " --> pdb=" O SER F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 232 through 249 removed outlier: 3.918A pdb=" N GLY F 236 " --> pdb=" O THR F 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY F 249 " --> pdb=" O ILE F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 256 Processing helix chain 'F' and resid 260 through 272 Processing helix chain 'F' and resid 311 through 324 Processing helix chain 'F' and resid 330 through 337 Processing helix chain 'F' and resid 355 through 376 removed outlier: 3.731A pdb=" N HIS F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 393 Processing helix chain 'F' and resid 394 through 397 removed outlier: 4.165A pdb=" N ILE F 397 " --> pdb=" O ASP F 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 394 through 397' Processing helix chain 'F' and resid 401 through 405 removed outlier: 3.691A pdb=" N LYS F 405 " --> pdb=" O ALA F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 412 removed outlier: 3.757A pdb=" N ALA F 412 " --> pdb=" O ILE F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 421 removed outlier: 3.651A pdb=" N LYS F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 433 removed outlier: 4.908A pdb=" N LEU F 431 " --> pdb=" O PHE F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 437 No H-bonds generated for 'chain 'F' and resid 435 through 437' Processing helix chain 'F' and resid 438 through 450 removed outlier: 3.814A pdb=" N LEU F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 448 " --> pdb=" O ILE F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 482 Processing helix chain 'F' and resid 558 through 577 Processing helix chain 'F' and resid 583 through 588 Processing helix chain 'F' and resid 590 through 595 removed outlier: 4.361A pdb=" N LYS F 595 " --> pdb=" O ILE F 591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 343 removed outlier: 7.803A pdb=" N TYR A 521 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA A 351 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 460 removed outlier: 6.018A pdb=" N TYR A 456 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N CYS A 554 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 458 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 120 Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 342 Processing sheet with id=AA7, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 460 removed outlier: 6.520A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 341 through 343 Processing sheet with id=AB1, first strand: chain 'E' and resid 398 through 400 Processing sheet with id=AB2, first strand: chain 'E' and resid 455 through 456 Processing sheet with id=AB3, first strand: chain 'E' and resid 501 through 504 Processing sheet with id=AB4, first strand: chain 'F' and resid 338 through 343 Processing sheet with id=AB5, first strand: chain 'F' and resid 455 through 458 removed outlier: 6.744A pdb=" N VAL F 552 " --> pdb=" O VAL F 457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 502 through 503 removed outlier: 3.868A pdb=" N LEU F 549 " --> pdb=" O ILE F 503 " (cutoff:3.500A) 663 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4127 1.34 - 1.46: 2160 1.46 - 1.58: 5155 1.58 - 1.70: 21 1.70 - 1.81: 45 Bond restraints: 11508 Sorted by residual: bond pdb=" O3' G J 9 " pdb=" P C J 10 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.50e-02 4.44e+03 6.28e+00 bond pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 1.515 1.505 0.009 6.20e-03 2.60e+04 2.30e+00 bond pdb=" O4' C J 7 " pdb=" C1' C J 7 " ideal model delta sigma weight residual 1.412 1.393 0.019 1.50e-02 4.44e+03 1.57e+00 bond pdb=" CG GLN A 271 " pdb=" CD GLN A 271 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" C4' C J 10 " pdb=" O4' C J 10 " ideal model delta sigma weight residual 1.454 1.436 0.018 1.50e-02 4.44e+03 1.44e+00 ... (remaining 11503 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.96: 321 106.96 - 113.75: 6405 113.75 - 120.54: 4567 120.54 - 127.34: 4457 127.34 - 134.13: 85 Bond angle restraints: 15835 Sorted by residual: angle pdb=" CA TYR B 315 " pdb=" CB TYR B 315 " pdb=" CG TYR B 315 " ideal model delta sigma weight residual 113.90 120.20 -6.30 1.80e+00 3.09e-01 1.23e+01 angle pdb=" C ASP B 314 " pdb=" N TYR B 315 " pdb=" CA TYR B 315 " ideal model delta sigma weight residual 121.14 115.13 6.01 1.75e+00 3.27e-01 1.18e+01 angle pdb=" C3' A K 9 " pdb=" O3' A K 9 " pdb=" P C K 10 " ideal model delta sigma weight residual 120.20 125.02 -4.82 1.50e+00 4.44e-01 1.03e+01 angle pdb=" CA TYR A 315 " pdb=" CB TYR A 315 " pdb=" CG TYR A 315 " ideal model delta sigma weight residual 113.90 119.53 -5.63 1.80e+00 3.09e-01 9.79e+00 angle pdb=" C4' C J 7 " pdb=" C3' C J 7 " pdb=" C2' C J 7 " ideal model delta sigma weight residual 102.60 105.71 -3.11 1.00e+00 1.00e+00 9.65e+00 ... (remaining 15830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 6715 35.78 - 71.56: 72 71.56 - 107.33: 16 107.33 - 143.11: 3 143.11 - 178.89: 4 Dihedral angle restraints: 6810 sinusoidal: 1523 harmonic: 5287 Sorted by residual: dihedral pdb=" O4' C K 11 " pdb=" C1' C K 11 " pdb=" N1 C K 11 " pdb=" C2 C K 11 " ideal model delta sinusoidal sigma weight residual 200.00 57.53 142.47 1 1.50e+01 4.44e-03 7.65e+01 dihedral pdb=" O4' C J 10 " pdb=" C1' C J 10 " pdb=" N1 C J 10 " pdb=" C2 C J 10 " ideal model delta sinusoidal sigma weight residual 232.00 62.23 169.77 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' C K 7 " pdb=" C1' C K 7 " pdb=" N1 C K 7 " pdb=" C2 C K 7 " ideal model delta sinusoidal sigma weight residual 232.00 62.68 169.32 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 6807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1297 0.042 - 0.084: 476 0.084 - 0.125: 166 0.125 - 0.167: 9 0.167 - 0.209: 4 Chirality restraints: 1952 Sorted by residual: chirality pdb=" C3' A K 9 " pdb=" C4' A K 9 " pdb=" O3' A K 9 " pdb=" C2' A K 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA TYR B 315 " pdb=" N TYR B 315 " pdb=" C TYR B 315 " pdb=" CB TYR B 315 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C3' C J 10 " pdb=" C4' C J 10 " pdb=" O3' C J 10 " pdb=" C2' C J 10 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 1949 not shown) Planarity restraints: 2129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 368 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C SER A 368 " 0.055 2.00e-02 2.50e+03 pdb=" O SER A 368 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 369 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 360 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C TYR A 360 " -0.054 2.00e-02 2.50e+03 pdb=" O TYR A 360 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP A 361 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 366 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C ARG A 366 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG A 366 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 367 " 0.017 2.00e-02 2.50e+03 ... (remaining 2126 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1836 2.75 - 3.29: 10962 3.29 - 3.83: 18434 3.83 - 4.36: 19678 4.36 - 4.90: 33905 Nonbonded interactions: 84815 Sorted by model distance: nonbonded pdb=" O TYR B 155 " pdb=" NH2 ARG B 451 " model vdw 2.217 2.520 nonbonded pdb=" NE1 TRP A 285 " pdb=" O ARG A 290 " model vdw 2.227 2.520 nonbonded pdb=" NH2 ARG B 194 " pdb=" OD1 ASP B 264 " model vdw 2.231 2.520 nonbonded pdb=" O GLU B 292 " pdb=" OG SER B 295 " model vdw 2.233 2.440 nonbonded pdb=" NH2 ARG B 143 " pdb=" O HIS B 210 " model vdw 2.240 2.520 ... (remaining 84810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 115 through 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 or (resid 125 through 150 and (name N or name CA or \ name C or name O or name CB )) or resid 151 through 153 or (resid 154 through 1 \ 58 and (name N or name CA or name C or name O or name CB )) or (resid 159 throug \ h 169 and (name N or name CA or name C or name O or name CB )) or resid 170 or ( \ resid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 \ or (resid 173 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 through 182 and (name N or name CA or name C or na \ me O or name CB )) or (resid 183 through 202 and (name N or name CA or name C or \ name O or name CB )) or resid 203 or (resid 204 through 208 and (name N or name \ CA or name C or name O or name CB )) or resid 209 or (resid 210 and (name N or \ name CA or name C or name O or name CB )) or resid 211 or (resid 212 through 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 or (resid \ 220 through 235 and (name N or name CA or name C or name O or name CB )) or res \ id 236 or (resid 237 through 248 and (name N or name CA or name C or name O or n \ ame CB )) or resid 249 or (resid 250 through 257 and (name N or name CA or name \ C or name O or name CB )) or resid 258 or (resid 259 through 273 and (name N or \ name CA or name C or name O or name CB )) or resid 274 or (resid 275 through 288 \ and (name N or name CA or name C or name O or name CB )) or resid 289 or (resid \ 290 through 295 and (name N or name CA or name C or name O or name CB )) or (re \ sid 310 through 323 and (name N or name CA or name C or name O or name CB )) or \ resid 324 or (resid 325 through 356 and (name N or name CA or name C or name O o \ r name CB )) or resid 357 or (resid 358 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 through 400 and (name N \ or name CA or name C or name O or name CB )) or (resid 401 through 457 and (name \ N or name CA or name C or name O or name CB )) or resid 458 through 504 or resi \ d 548 through 602)) selection = (chain 'B' and ((resid 115 through 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 or (resid 125 through 150 and (name N or name CA or \ name C or name O or name CB )) or resid 151 through 153 or (resid 154 through 1 \ 58 and (name N or name CA or name C or name O or name CB )) or (resid 159 throug \ h 169 and (name N or name CA or name C or name O or name CB )) or resid 170 or ( \ resid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 \ or (resid 173 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 through 182 and (name N or name CA or name C or na \ me O or name CB )) or resid 183 or (resid 184 through 202 and (name N or name CA \ or name C or name O or name CB )) or resid 203 or (resid 204 through 208 and (n \ ame N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 an \ d (name N or name CA or name C or name O or name CB )) or resid 211 or (resid 21 \ 2 through 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 or (resid 220 through 235 and (name N or name CA or name C or name O or name \ CB )) or resid 236 or (resid 237 through 248 and (name N or name CA or name C o \ r name O or name CB )) or resid 249 or (resid 250 through 257 and (name N or nam \ e CA or name C or name O or name CB )) or resid 258 or (resid 259 through 273 an \ d (name N or name CA or name C or name O or name CB )) or resid 274 or (resid 27 \ 5 through 288 and (name N or name CA or name C or name O or name CB )) or resid \ 289 or (resid 290 through 295 and (name N or name CA or name C or name O or name \ CB )) or (resid 310 through 323 and (name N or name CA or name C or name O or n \ ame CB )) or resid 324 or (resid 325 through 356 and (name N or name CA or name \ C or name O or name CB )) or resid 357 or (resid 358 through 378 and (name N or \ name CA or name C or name O or name CB )) or resid 379 or (resid 380 through 400 \ and (name N or name CA or name C or name O or name CB )) or (resid 401 through \ 457 and (name N or name CA or name C or name O or name CB )) or resid 458 throug \ h 504 or resid 548 through 602)) selection = (chain 'E' and (resid 115 through 295 or resid 310 through 504 or resid 548 thro \ ugh 602)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.860 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 33.210 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4809 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11508 Z= 0.312 Angle : 0.563 8.176 15835 Z= 0.315 Chirality : 0.046 0.209 1952 Planarity : 0.004 0.040 2129 Dihedral : 14.081 178.887 3374 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1808 helix: 1.07 (0.19), residues: 858 sheet: -0.57 (0.58), residues: 90 loop : -1.16 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 285 HIS 0.009 0.002 HIS A 162 PHE 0.012 0.002 PHE B 213 TYR 0.031 0.002 TYR B 315 ARG 0.007 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.143 Fit side-chains REVERT: A 180 HIS cc_start: 0.6012 (t-90) cc_final: 0.5803 (t-170) REVERT: A 227 PRO cc_start: 0.8597 (Cg_endo) cc_final: 0.8364 (Cg_exo) REVERT: A 230 LYS cc_start: 0.8627 (mttt) cc_final: 0.8143 (mttm) REVERT: A 239 MET cc_start: 0.7565 (mtp) cc_final: 0.7073 (mtp) REVERT: A 271 GLN cc_start: 0.7825 (mt0) cc_final: 0.7434 (mt0) REVERT: A 329 PHE cc_start: 0.8122 (t80) cc_final: 0.7722 (t80) REVERT: A 348 ARG cc_start: 0.6135 (mtm180) cc_final: 0.5665 (mtp85) REVERT: A 371 ARG cc_start: 0.6908 (ptm-80) cc_final: 0.6210 (ttp80) REVERT: A 417 GLU cc_start: 0.7473 (tt0) cc_final: 0.6934 (tt0) REVERT: A 429 GLU cc_start: 0.6438 (tt0) cc_final: 0.5919 (mt-10) REVERT: B 164 ARG cc_start: 0.7382 (mmt180) cc_final: 0.7114 (mmt180) REVERT: B 240 MET cc_start: 0.8088 (tpp) cc_final: 0.7504 (tpp) REVERT: B 255 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6892 (mt-10) REVERT: B 271 GLN cc_start: 0.7126 (mt0) cc_final: 0.6886 (mt0) REVERT: B 331 TYR cc_start: 0.6763 (p90) cc_final: 0.6546 (p90) REVERT: B 339 ARG cc_start: 0.6890 (mtp85) cc_final: 0.6440 (ptm160) REVERT: B 421 LYS cc_start: 0.8079 (mtmt) cc_final: 0.6945 (mptt) REVERT: B 435 ASP cc_start: 0.7384 (t0) cc_final: 0.6802 (t0) REVERT: B 437 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7395 (mttm) REVERT: B 439 LYS cc_start: 0.6834 (tttt) cc_final: 0.6541 (tttm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2569 time to fit residues: 53.8140 Evaluate side-chains 129 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 93 optimal weight: 50.0000 chunk 73 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 375 GLN A 425 ASN B 210 HIS B 358 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4834 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11508 Z= 0.332 Angle : 0.573 9.444 15835 Z= 0.304 Chirality : 0.047 0.223 1952 Planarity : 0.004 0.039 2129 Dihedral : 13.311 179.064 2075 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.48 % Allowed : 10.28 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1808 helix: 1.06 (0.18), residues: 872 sheet: -0.39 (0.59), residues: 88 loop : -1.13 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 285 HIS 0.009 0.001 HIS A 162 PHE 0.012 0.002 PHE B 221 TYR 0.030 0.002 TYR B 315 ARG 0.004 0.001 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.301 Fit side-chains REVERT: A 227 PRO cc_start: 0.8634 (Cg_endo) cc_final: 0.8417 (Cg_exo) REVERT: A 230 LYS cc_start: 0.8633 (mttt) cc_final: 0.8023 (mttm) REVERT: A 239 MET cc_start: 0.7403 (mtp) cc_final: 0.6775 (mtp) REVERT: A 271 GLN cc_start: 0.7863 (mt0) cc_final: 0.7433 (mt0) REVERT: A 329 PHE cc_start: 0.8097 (t80) cc_final: 0.7697 (t80) REVERT: A 348 ARG cc_start: 0.6377 (mtm180) cc_final: 0.5826 (mtp85) REVERT: A 371 ARG cc_start: 0.7092 (ptm-80) cc_final: 0.6478 (ttp-170) REVERT: A 406 LYS cc_start: 0.7031 (mmtt) cc_final: 0.6813 (mttp) REVERT: A 417 GLU cc_start: 0.7517 (tt0) cc_final: 0.7030 (tt0) REVERT: A 429 GLU cc_start: 0.6845 (tt0) cc_final: 0.6209 (mt-10) REVERT: A 437 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7779 (mmtm) REVERT: B 190 GLN cc_start: 0.6824 (mt0) cc_final: 0.6604 (mm-40) REVERT: B 195 ASP cc_start: 0.6552 (m-30) cc_final: 0.6345 (m-30) REVERT: B 255 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7019 (mt-10) REVERT: B 331 TYR cc_start: 0.6781 (p90) cc_final: 0.6580 (p90) REVERT: B 339 ARG cc_start: 0.6933 (mtp85) cc_final: 0.6488 (ptm160) REVERT: B 383 ASP cc_start: 0.7106 (m-30) cc_final: 0.6770 (m-30) REVERT: B 421 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7068 (mttp) REVERT: B 435 ASP cc_start: 0.7346 (t0) cc_final: 0.6740 (t0) REVERT: B 437 LYS cc_start: 0.7671 (mtmt) cc_final: 0.7451 (mttm) outliers start: 14 outliers final: 11 residues processed: 145 average time/residue: 0.2404 time to fit residues: 49.6967 Evaluate side-chains 139 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 137 optimal weight: 50.0000 chunk 112 optimal weight: 40.0000 chunk 45 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 30.0000 chunk 164 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 180 HIS A 303 ASN B 210 HIS B 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4903 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.077 11508 Z= 0.650 Angle : 0.744 9.040 15835 Z= 0.395 Chirality : 0.052 0.261 1952 Planarity : 0.005 0.051 2129 Dihedral : 13.216 176.162 2075 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.63 % Favored : 91.32 % Rotamer: Outliers : 3.90 % Allowed : 12.41 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1808 helix: 0.41 (0.18), residues: 873 sheet: -0.48 (0.57), residues: 86 loop : -1.53 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 285 HIS 0.026 0.003 HIS B 210 PHE 0.014 0.003 PHE B 213 TYR 0.033 0.003 TYR B 315 ARG 0.010 0.001 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.334 Fit side-chains REVERT: A 150 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8454 (mm) REVERT: A 230 LYS cc_start: 0.8643 (mttt) cc_final: 0.8004 (mttm) REVERT: A 239 MET cc_start: 0.7306 (mtp) cc_final: 0.6539 (mtp) REVERT: A 371 ARG cc_start: 0.7148 (ptm-80) cc_final: 0.6671 (ttp-170) REVERT: A 417 GLU cc_start: 0.7641 (tt0) cc_final: 0.7215 (tt0) REVERT: A 429 GLU cc_start: 0.6991 (tt0) cc_final: 0.6303 (mt-10) REVERT: A 437 LYS cc_start: 0.8483 (mtmt) cc_final: 0.7833 (mmtm) REVERT: B 190 GLN cc_start: 0.7028 (mt0) cc_final: 0.6759 (mm-40) REVERT: B 195 ASP cc_start: 0.6631 (m-30) cc_final: 0.6428 (m-30) REVERT: B 220 ARG cc_start: 0.5948 (OUTLIER) cc_final: 0.5573 (tpt170) REVERT: B 255 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7028 (mt-10) REVERT: B 331 TYR cc_start: 0.6812 (p90) cc_final: 0.6589 (p90) REVERT: B 339 ARG cc_start: 0.6799 (mtp85) cc_final: 0.6514 (ptm160) REVERT: B 372 ARG cc_start: 0.6917 (mmt-90) cc_final: 0.6004 (mmm-85) REVERT: B 383 ASP cc_start: 0.7400 (m-30) cc_final: 0.7158 (m-30) REVERT: B 421 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7050 (mttt) REVERT: B 435 ASP cc_start: 0.7584 (t0) cc_final: 0.6940 (t70) REVERT: B 437 LYS cc_start: 0.7794 (mtmt) cc_final: 0.7537 (mttm) REVERT: B 439 LYS cc_start: 0.7368 (tttt) cc_final: 0.7065 (tttm) outliers start: 22 outliers final: 16 residues processed: 140 average time/residue: 0.2617 time to fit residues: 50.9716 Evaluate side-chains 139 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 50.0000 chunk 124 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 chunk 166 optimal weight: 0.0070 chunk 175 optimal weight: 0.3980 chunk 86 optimal weight: 9.9990 chunk 157 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS A 246 ASN B 119 ASN B 210 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4806 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11508 Z= 0.166 Angle : 0.492 8.895 15835 Z= 0.263 Chirality : 0.044 0.202 1952 Planarity : 0.003 0.046 2129 Dihedral : 12.870 179.298 2075 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.84 % Allowed : 13.30 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1808 helix: 1.12 (0.18), residues: 885 sheet: -0.31 (0.59), residues: 88 loop : -1.05 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 285 HIS 0.012 0.001 HIS B 210 PHE 0.015 0.001 PHE B 221 TYR 0.024 0.001 TYR A 315 ARG 0.003 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.259 Fit side-chains REVERT: A 149 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: A 227 PRO cc_start: 0.8629 (Cg_endo) cc_final: 0.8414 (Cg_exo) REVERT: A 230 LYS cc_start: 0.8642 (mttt) cc_final: 0.8121 (mttm) REVERT: A 235 GLN cc_start: 0.7803 (mt0) cc_final: 0.6452 (mp10) REVERT: A 239 MET cc_start: 0.7505 (mtp) cc_final: 0.6966 (mtp) REVERT: A 271 GLN cc_start: 0.7687 (mt0) cc_final: 0.7312 (mt0) REVERT: A 371 ARG cc_start: 0.7031 (ptm-80) cc_final: 0.6461 (ttp-170) REVERT: A 429 GLU cc_start: 0.6972 (tt0) cc_final: 0.6297 (mt-10) REVERT: A 437 LYS cc_start: 0.8486 (mtmt) cc_final: 0.7806 (mmtm) REVERT: B 190 GLN cc_start: 0.6988 (mt0) cc_final: 0.6705 (mm-40) REVERT: B 255 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6920 (mt-10) REVERT: B 339 ARG cc_start: 0.6791 (mtp85) cc_final: 0.6423 (ptm160) REVERT: B 372 ARG cc_start: 0.6615 (mmt-90) cc_final: 0.5958 (mmm-85) REVERT: B 376 HIS cc_start: 0.7908 (t-90) cc_final: 0.7516 (t-90) REVERT: B 421 LYS cc_start: 0.8052 (mtmt) cc_final: 0.6853 (mptt) REVERT: B 435 ASP cc_start: 0.7370 (t0) cc_final: 0.6699 (t70) REVERT: B 437 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7496 (mttm) outliers start: 16 outliers final: 9 residues processed: 141 average time/residue: 0.2427 time to fit residues: 48.6027 Evaluate side-chains 134 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.0980 chunk 99 optimal weight: 30.0000 chunk 2 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 0.0970 chunk 121 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 157 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 125 HIS A 180 HIS A 246 ASN B 210 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4847 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11508 Z= 0.341 Angle : 0.555 8.669 15835 Z= 0.296 Chirality : 0.046 0.221 1952 Planarity : 0.004 0.044 2129 Dihedral : 12.890 179.403 2075 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.90 % Allowed : 14.18 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1808 helix: 1.09 (0.18), residues: 875 sheet: -0.29 (0.59), residues: 88 loop : -1.08 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 285 HIS 0.008 0.002 HIS A 162 PHE 0.043 0.003 PHE A 329 TYR 0.027 0.002 TYR B 315 ARG 0.006 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.258 Fit side-chains REVERT: A 149 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: A 230 LYS cc_start: 0.8657 (mttt) cc_final: 0.8036 (mttm) REVERT: A 239 MET cc_start: 0.7408 (mtp) cc_final: 0.6785 (mtp) REVERT: A 271 GLN cc_start: 0.7852 (mt0) cc_final: 0.7439 (mt0) REVERT: A 371 ARG cc_start: 0.7052 (ptm-80) cc_final: 0.6437 (ttp-170) REVERT: A 429 GLU cc_start: 0.6997 (tt0) cc_final: 0.6328 (mt-10) REVERT: A 437 LYS cc_start: 0.8514 (mtmt) cc_final: 0.7821 (mmtm) REVERT: B 190 GLN cc_start: 0.6999 (mt0) cc_final: 0.6797 (mm-40) REVERT: B 255 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6987 (mt-10) REVERT: B 339 ARG cc_start: 0.6821 (mtp85) cc_final: 0.6545 (ptm160) REVERT: B 372 ARG cc_start: 0.6737 (mmt-90) cc_final: 0.5988 (mmm-85) REVERT: B 421 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7012 (mttp) REVERT: B 435 ASP cc_start: 0.7377 (t0) cc_final: 0.6575 (t0) outliers start: 22 outliers final: 18 residues processed: 141 average time/residue: 0.2426 time to fit residues: 48.8294 Evaluate side-chains 143 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 34 optimal weight: 0.0870 chunk 103 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 176 optimal weight: 0.0020 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 14 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 50.0000 overall best weight: 0.8768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS B 210 HIS B 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4812 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11508 Z= 0.193 Angle : 0.491 8.612 15835 Z= 0.262 Chirality : 0.044 0.208 1952 Planarity : 0.003 0.044 2129 Dihedral : 12.829 179.969 2075 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.01 % Allowed : 15.25 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1808 helix: 1.36 (0.18), residues: 873 sheet: -0.17 (0.59), residues: 88 loop : -1.01 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 285 HIS 0.010 0.001 HIS B 210 PHE 0.033 0.002 PHE B 329 TYR 0.024 0.001 TYR A 315 ARG 0.003 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.288 Fit side-chains REVERT: A 149 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: A 227 PRO cc_start: 0.8636 (Cg_endo) cc_final: 0.8410 (Cg_exo) REVERT: A 230 LYS cc_start: 0.8636 (mttt) cc_final: 0.8001 (mttm) REVERT: A 239 MET cc_start: 0.7472 (mtp) cc_final: 0.6965 (mtp) REVERT: A 271 GLN cc_start: 0.7798 (mt0) cc_final: 0.7299 (mt0) REVERT: A 371 ARG cc_start: 0.7036 (ptm-80) cc_final: 0.6388 (ptt-90) REVERT: A 429 GLU cc_start: 0.6905 (tt0) cc_final: 0.6203 (mt-10) REVERT: A 437 LYS cc_start: 0.8495 (mtmt) cc_final: 0.7801 (mmtm) REVERT: B 190 GLN cc_start: 0.7067 (mt0) cc_final: 0.6795 (mm-40) REVERT: B 220 ARG cc_start: 0.5605 (OUTLIER) cc_final: 0.5264 (tpt170) REVERT: B 255 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6885 (mt-10) REVERT: B 339 ARG cc_start: 0.6795 (mtp85) cc_final: 0.6403 (ptm160) REVERT: B 372 ARG cc_start: 0.6607 (mmt-90) cc_final: 0.5954 (mmm-85) REVERT: B 383 ASP cc_start: 0.7025 (m-30) cc_final: 0.6616 (m-30) REVERT: B 421 LYS cc_start: 0.7970 (mtmt) cc_final: 0.6858 (mptt) REVERT: B 435 ASP cc_start: 0.7354 (t0) cc_final: 0.6543 (t0) outliers start: 17 outliers final: 12 residues processed: 138 average time/residue: 0.2509 time to fit residues: 48.8908 Evaluate side-chains 137 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 128 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 175 optimal weight: 0.0770 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS B 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4842 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11508 Z= 0.328 Angle : 0.545 7.969 15835 Z= 0.290 Chirality : 0.046 0.219 1952 Planarity : 0.004 0.042 2129 Dihedral : 12.900 179.864 2075 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.08 % Allowed : 15.07 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1808 helix: 1.27 (0.18), residues: 867 sheet: -0.23 (0.58), residues: 88 loop : -1.08 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 285 HIS 0.010 0.002 HIS B 376 PHE 0.035 0.002 PHE B 329 TYR 0.027 0.002 TYR B 315 ARG 0.005 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.014 Fit side-chains REVERT: A 149 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: A 150 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8376 (mm) REVERT: A 227 PRO cc_start: 0.8653 (Cg_endo) cc_final: 0.8431 (Cg_exo) REVERT: A 230 LYS cc_start: 0.8697 (mttt) cc_final: 0.8076 (mttm) REVERT: A 239 MET cc_start: 0.7371 (mtp) cc_final: 0.6665 (mtp) REVERT: A 271 GLN cc_start: 0.7812 (mt0) cc_final: 0.7361 (mt0) REVERT: A 348 ARG cc_start: 0.6399 (mtm180) cc_final: 0.6030 (mtp85) REVERT: A 371 ARG cc_start: 0.7048 (ptm-80) cc_final: 0.6448 (ttp-170) REVERT: A 429 GLU cc_start: 0.6927 (tt0) cc_final: 0.6230 (mt-10) REVERT: A 437 LYS cc_start: 0.8518 (mtmt) cc_final: 0.7814 (mmtm) REVERT: B 190 GLN cc_start: 0.7030 (mt0) cc_final: 0.6821 (mm-40) REVERT: B 220 ARG cc_start: 0.5636 (OUTLIER) cc_final: 0.5301 (tpt170) REVERT: B 255 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6943 (mt-10) REVERT: B 339 ARG cc_start: 0.6812 (mtp85) cc_final: 0.6325 (ptm160) REVERT: B 383 ASP cc_start: 0.7207 (m-30) cc_final: 0.6769 (m-30) REVERT: B 421 LYS cc_start: 0.8022 (mtmt) cc_final: 0.7005 (mttp) REVERT: B 435 ASP cc_start: 0.7379 (t0) cc_final: 0.6572 (t0) outliers start: 23 outliers final: 17 residues processed: 139 average time/residue: 0.2661 time to fit residues: 53.4897 Evaluate side-chains 139 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 137 optimal weight: 50.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS B 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4835 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11508 Z= 0.290 Angle : 0.527 7.639 15835 Z= 0.282 Chirality : 0.045 0.217 1952 Planarity : 0.004 0.043 2129 Dihedral : 12.904 179.888 2075 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.26 % Allowed : 15.25 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1808 helix: 1.31 (0.18), residues: 867 sheet: -0.17 (0.59), residues: 88 loop : -1.07 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 285 HIS 0.009 0.002 HIS B 376 PHE 0.048 0.002 PHE A 329 TYR 0.025 0.002 TYR B 315 ARG 0.004 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.246 Fit side-chains REVERT: A 149 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7395 (tt0) REVERT: A 150 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8392 (mm) REVERT: A 227 PRO cc_start: 0.8653 (Cg_endo) cc_final: 0.8428 (Cg_exo) REVERT: A 230 LYS cc_start: 0.8701 (mttt) cc_final: 0.8057 (mttm) REVERT: A 239 MET cc_start: 0.7423 (mtp) cc_final: 0.6853 (mtp) REVERT: A 271 GLN cc_start: 0.7827 (mt0) cc_final: 0.7363 (mt0) REVERT: A 348 ARG cc_start: 0.6390 (mtm180) cc_final: 0.5794 (mtp85) REVERT: A 371 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6507 (ttp-170) REVERT: A 429 GLU cc_start: 0.6925 (tt0) cc_final: 0.6217 (mt-10) REVERT: A 437 LYS cc_start: 0.8517 (mtmt) cc_final: 0.7810 (mmtm) REVERT: B 190 GLN cc_start: 0.7124 (mt0) cc_final: 0.6846 (mm-40) REVERT: B 220 ARG cc_start: 0.5578 (OUTLIER) cc_final: 0.5268 (tpt170) REVERT: B 255 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6922 (mt-10) REVERT: B 339 ARG cc_start: 0.6820 (mtp85) cc_final: 0.6325 (ptm160) REVERT: B 383 ASP cc_start: 0.7214 (m-30) cc_final: 0.6777 (m-30) REVERT: B 421 LYS cc_start: 0.8017 (mtmt) cc_final: 0.6986 (mttp) REVERT: B 435 ASP cc_start: 0.7383 (t0) cc_final: 0.6572 (t0) outliers start: 24 outliers final: 17 residues processed: 140 average time/residue: 0.2548 time to fit residues: 51.1646 Evaluate side-chains 142 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 50.0000 chunk 168 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 98 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 chunk 147 optimal weight: 30.0000 chunk 154 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS B 210 HIS B 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4896 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 11508 Z= 0.592 Angle : 0.684 8.764 15835 Z= 0.365 Chirality : 0.050 0.241 1952 Planarity : 0.005 0.046 2129 Dihedral : 13.060 176.714 2075 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.46 % Favored : 91.48 % Rotamer: Outliers : 4.79 % Allowed : 15.07 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.20), residues: 1808 helix: 0.71 (0.18), residues: 860 sheet: -0.35 (0.58), residues: 87 loop : -1.36 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 313 HIS 0.014 0.003 HIS B 210 PHE 0.043 0.003 PHE B 329 TYR 0.035 0.003 TYR B 315 ARG 0.008 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.246 Fit side-chains REVERT: A 149 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: A 150 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8342 (mm) REVERT: A 227 PRO cc_start: 0.8671 (Cg_endo) cc_final: 0.8447 (Cg_exo) REVERT: A 230 LYS cc_start: 0.8714 (mttt) cc_final: 0.8071 (mttm) REVERT: A 239 MET cc_start: 0.7331 (mtp) cc_final: 0.6635 (mtp) REVERT: A 429 GLU cc_start: 0.7009 (tt0) cc_final: 0.6319 (mt-10) REVERT: A 437 LYS cc_start: 0.8509 (mtmt) cc_final: 0.7849 (mmtm) REVERT: B 190 GLN cc_start: 0.7142 (mt0) cc_final: 0.6942 (mm-40) REVERT: B 220 ARG cc_start: 0.5721 (OUTLIER) cc_final: 0.5499 (tpt170) REVERT: B 255 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6980 (mt-10) REVERT: B 339 ARG cc_start: 0.6724 (mtp85) cc_final: 0.6465 (ptm160) REVERT: B 372 ARG cc_start: 0.6790 (mmt-90) cc_final: 0.5932 (mmm-85) REVERT: B 383 ASP cc_start: 0.7351 (m-30) cc_final: 0.6930 (m-30) REVERT: B 421 LYS cc_start: 0.8070 (mtmt) cc_final: 0.6919 (mptt) REVERT: B 435 ASP cc_start: 0.7563 (t0) cc_final: 0.6734 (t0) REVERT: B 439 LYS cc_start: 0.7385 (tttt) cc_final: 0.7071 (tttm) outliers start: 27 outliers final: 19 residues processed: 140 average time/residue: 0.2603 time to fit residues: 51.8159 Evaluate side-chains 140 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 7.9990 chunk 172 optimal weight: 0.6980 chunk 105 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS B 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4865 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11508 Z= 0.375 Angle : 0.577 7.458 15835 Z= 0.310 Chirality : 0.047 0.225 1952 Planarity : 0.004 0.045 2129 Dihedral : 12.968 177.498 2075 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.26 % Allowed : 15.43 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1808 helix: 0.85 (0.18), residues: 867 sheet: 0.09 (0.64), residues: 71 loop : -1.28 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 285 HIS 0.010 0.002 HIS B 376 PHE 0.059 0.003 PHE A 329 TYR 0.028 0.002 TYR B 315 ARG 0.005 0.001 ARG A 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 2.356 Fit side-chains REVERT: A 149 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: A 150 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8359 (mm) REVERT: A 230 LYS cc_start: 0.8726 (mttt) cc_final: 0.8064 (mttm) REVERT: A 239 MET cc_start: 0.7359 (mtp) cc_final: 0.6668 (mtp) REVERT: A 271 GLN cc_start: 0.7842 (mt0) cc_final: 0.7425 (mt0) REVERT: A 348 ARG cc_start: 0.6576 (mtm180) cc_final: 0.6206 (mtp85) REVERT: A 371 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6585 (ttp-170) REVERT: A 429 GLU cc_start: 0.6947 (tt0) cc_final: 0.6245 (mt-10) REVERT: A 437 LYS cc_start: 0.8524 (mtmt) cc_final: 0.7830 (mmtm) REVERT: B 190 GLN cc_start: 0.7094 (mm110) cc_final: 0.6884 (mm-40) REVERT: B 220 ARG cc_start: 0.5600 (OUTLIER) cc_final: 0.5319 (tpt170) REVERT: B 255 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6953 (mt-10) REVERT: B 339 ARG cc_start: 0.6794 (mtp85) cc_final: 0.6529 (ptm160) REVERT: B 421 LYS cc_start: 0.8046 (mtmt) cc_final: 0.6986 (mttp) REVERT: B 435 ASP cc_start: 0.7401 (t0) cc_final: 0.6693 (t70) outliers start: 24 outliers final: 19 residues processed: 142 average time/residue: 0.2476 time to fit residues: 50.2616 Evaluate side-chains 145 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 133 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 60 optimal weight: 0.3980 chunk 148 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS B 210 HIS B 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.263766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.179998 restraints weight = 12101.851| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.76 r_work: 0.3708 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11508 Z= 0.163 Angle : 0.481 7.724 15835 Z= 0.258 Chirality : 0.044 0.207 1952 Planarity : 0.003 0.046 2129 Dihedral : 12.849 179.410 2075 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.84 % Allowed : 16.84 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.20), residues: 1808 helix: 1.34 (0.18), residues: 878 sheet: -0.19 (0.59), residues: 88 loop : -1.07 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 285 HIS 0.015 0.002 HIS B 210 PHE 0.040 0.002 PHE B 329 TYR 0.021 0.001 TYR A 315 ARG 0.005 0.000 ARG A 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2384.94 seconds wall clock time: 43 minutes 53.08 seconds (2633.08 seconds total)